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- PDB-3gqg: Crystal structure at acidic pH of the ferric form of the Root eff... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3gqg | ||||||
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Title | Crystal structure at acidic pH of the ferric form of the Root effect hemoglobin from Trematomus bernacchii. | ||||||
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![]() | OXYGEN TRANSPORT / pentacoordinate high-spin Fe(III) form / antacrtic fish hemoglobin / Acetylation / Heme / Iron / Metal-binding / Transport | ||||||
Function / homology | ![]() haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vergara, A. / Franzese, M. / Merlino, A. / Bonomi, G. / Mazzarella, L. | ||||||
![]() | ![]() Title: Correlation between hemichrome stability and the root effect in tetrameric hemoglobins. Authors: Vergara, A. / Franzese, M. / Merlino, A. / Bonomi, G. / Verde, C. / Giordano, D. / di Prisco, G. / Lee, H.C. / Peisach, J. / Mazzarella, L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 137 KB | Display | ![]() |
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PDB format | ![]() | 105.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 28.7 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2h8fS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | tetramer |
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Components
#1: Protein | Mass: 15683.271 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Protein | Mass: 16153.368 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 298 K / Method: liquid diffusion / pH: 6 Details: Crystallization of oxidized Hb from trematomus bernacchii was carried out in capillary at pH6 and room temperature by liquid diffusion technique (final crystallization conditions were 1.5 ...Details: Crystallization of oxidized Hb from trematomus bernacchii was carried out in capillary at pH6 and room temperature by liquid diffusion technique (final crystallization conditions were 1.5 mg/ml protein and 8% w/v MPEG 5K)., pH 6.0, LIQUID DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 14, 2005 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→13.9 Å / Num. all: 69281 / Num. obs: 69281 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 |
Reflection shell | Resolution: 1.73→1.76 Å / Rmerge(I) obs: 0.175 / % possible all: 88.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB code 2H8F Resolution: 1.73→13.9 Å Isotropic thermal model: Isotropic. Anisotropic thermal model has been used for iron atoms. Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Please note that the collected diffraction data show pseudo-merohedral twinning. The twin fractions, determined by the algorithm implemented in the progream SHELX is almost 0.50.
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Refinement step | Cycle: LAST / Resolution: 1.73→13.9 Å
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